They probably won't line up. One thing you might want to consider is just making a one off out of fiberglass. Seems like a lot of work, but if you're going through the trouble of decking her out as a cafe racer, then a little custom fabrication won't hurt, and would actually make the bike more unique.
Another option would be to just use a flat oval with numbers on it for your side covers. The model year number would be cool. I've seen plenty of cafe bikes like that, and I actually like that race ready look. Carpy's done that on a lot of his: